The human phenotype ontology (HPO) intends to offer a tool that will allow large-scale computational analysis of the human phenome. The HPO currently contains over 9500 terms, each of which describes an individual phenotypic anomaly. The terms are arranged in a directed acyclic graph and are connected by “is-a” edges, such that a term represents a more specific or limited instance of its parent term(s). All relationships in the HPO are is_a relationships, i.e. a simple class-subclass relationships. For instance, Abnormality of the feet is_a Abnormality of the lower limbs. The relationships are transitive, meaning that they are inherited up all paths to the root. Organ abnormality is the main subontology of the HPO and contains descriptions of clinical abnormalities. Additional subontologies are provided to describe inheritance patterns and onset/clinical course.

A Web service that tags free text with ontology concepts. NCBO uses these Web services to annotate resources in the NCBO Resource Index to create an ontology index of these resources. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Our service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards.

NCBO

The NCBO Resource Web service is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data resources related to particular ontology concepts. The annotations are generated using the NCBO Annotator and presented through integration with BioPortal, enabling researchers to search for biomedical resources associated (annotated) with specific ontology terms. The NCBO Resources web service uses a concept recognizer (currently provided by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand these using ontology is_a relations in the ontology. The system's indexing workflow processes the text metadata of diverse resource elements such as gene expression data sets, descriptions of radiology images, clinical trial reports, and PubMed article abstracts to annotate and index them with concepts from appropriate ontologies. Researchers can then search biomedical data sources using ontology concepts.

NCBO

High level abstraction API (Java/REST/R) for interacting with ontology resources including local ontology files in standard OWL and OBO formats (via OWL API) and public ontology repositories: EBI Ontology Lookup Service (OLS) and NCBO BioPortal.

Tomasz Adamusiak, Helen Parkinson, Natalja Kurbatova, Misha Kapushesky, Morris Swertz

The aim of the SKELETOME project is to develop a community-driven, ontology-based knowledge curation platform for the skeletal dysplasia domain.

Tudor Groza